MolNFT v1 · #120097 · protein
Crystal structure of zikv NS5 methyltransferase in complex with GTP and sah
5GP1 · RNA-directed RNA polymerase NS5: “Crystal structure of zikv NS5 methyltransferase in complex with GTP and sah”. X-ray diffraction, 4 ligands (GTA, SAH, NI), 6 pockets (best druggability 0.76). MolNFT v1 #120097 on GenesisL1: 3D…
- PDB
- 5GP1
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase NS5
- UniProt
- H9A910
- Ligands
- GTA, SAH, NI, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase NS5 | protein | 262 | 37% helix, 17% strand | H9A910 |
| B | RNA-directed RNA polymerase NS5 | protein | 260 | 37% helix, 16% strand | H9A910 |
| C | RNA-directed RNA polymerase NS5 | protein | 261 | 36% helix, 17% strand | H9A910 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 3 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.76 | 0.78 | 104 | SAH |
| 2 | 675 | 0.68 | 0.77 | 46 | empty |
| 3 | 487 | 0.65 | 0.77 | 52 | SO4, SAH |
| 4 | 455 | 0.63 | 0.77 | 43 | SO4, SAH |
| 5 | 289 | 0.61 | 0.79 | 34 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 677 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GP1 · Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt H9A910
- Elsewhere: RCSB PDB 5GP1 · PDBe 5GP1 · UniProt H9A910
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